2025
Complete genome sequence of a novel Acinetobacter spp. linked to an outbreak of sepsis following apheresis platelet transfusion.
Kent A, Sula E, Breaker E, McAllister G, Gable P, Chan-Riley M, Leung V, Peaper D, Jones S, Jones J, Basavaraju S, Halpin A. Complete genome sequence of a novel Acinetobacter spp. linked to an outbreak of sepsis following apheresis platelet transfusion. Microbiology Resource Announcements 2025, e0136124. PMID: 40503797, DOI: 10.1128/mra.01361-24.Peer-Reviewed Original ResearchClassification of unsequenced Mycobacterium tuberculosis strains in a high-burden setting using a pairwise logistic regression approach
Rancu I, Sobkowiak B, Warren J, Ciobanu N, Codreanu A, Crudu V, Colijn C, Cohen T, Chitwood M. Classification of unsequenced Mycobacterium tuberculosis strains in a high-burden setting using a pairwise logistic regression approach. Access Microbiology 2025, 7: 000964.v3. PMID: 40519974, PMCID: PMC12163731, DOI: 10.1099/acmi.0.000964.v3.Peer-Reviewed Original ResearchWhole-genome sequencing dataSequence dataTransmission inferenceMolecular epidemiological studiesMycobacterium tuberculosis strainsTuberculosis strainsHigh-burden settingsFraction of individualsCulture-positive diseaseStrainTransmission clustersFraction of casesLow-burden settingsSNPsForeign-born migrantsTransmission dynamicsSequenceTuberculosis casesMycobacteriaClustersNotified tuberculosisAn affinity-based depletion strategy for evaluating the effects of ergothioneine on bacterial physiology
Seminara A, Hatzios S. An affinity-based depletion strategy for evaluating the effects of ergothioneine on bacterial physiology. Cell Chemical Biology 2025, 32: 486-497.e7. PMID: 40068683, PMCID: PMC12057763, DOI: 10.1016/j.chembiol.2025.02.004.Peer-Reviewed Original ResearchConceptsGastric pathogen Helicobacter pyloriHost-associated microbesOuter membrane transportersWild-type H. pyloriTransporter-deficient strainsPathogen Helicobacter pyloriNutrient-rich mediumBacterial physiologyMicrobial physiologyErgothioneine biosynthesisBacterial speciesMicrobial strainsComplex mediaCulture H. pyloriErgothioneineStrainHelicobacter pyloriPhysiologyH. pyloriComplicating effortsBiosynthesisTranscriptionFungalMicrobesHuman dietA new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission
Sobkowiak B, Cudahy P, Chitwood M, Clark T, Colijn C, Grandjean L, Walter K, Crudu V, Cohen T. A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission. Genome Medicine 2025, 17: 8. PMID: 39871355, PMCID: PMC11771024, DOI: 10.1186/s13073-025-01430-y.Peer-Reviewed Original ResearchConceptsShort-read WGS dataWhole-genome sequencingStrain sequencesWGS dataMultiple strainsStrain proportionsMycobacterium tuberculosis populationMixed infectionGenome sequenceBioinformatics pipelineClustering allele frequenciesDownstream analysisAllele frequenciesEvidence of mixed infectionSequenceTuberculosis populationStrainIsolatesIn vitroTransmission clustersMixed samplesAllelesInfectionMycobacterium tuberculosis infectionPathogens
2024
A predictive language model for SARS-CoV-2 evolution
Ma E, Guo X, Hu M, Wang P, Wang X, Wei C, Cheng G. A predictive language model for SARS-CoV-2 evolution. Signal Transduction And Targeted Therapy 2024, 9: 353. PMID: 39710752, PMCID: PMC11663983, DOI: 10.1038/s41392-024-02066-x.Peer-Reviewed Original ResearchConceptsSARS-CoV-2 evolutionHot mutation spotsFrequency of mutationsSequence dataS1 sequencesVital mutationsPredicted mutationsSARS-CoV-2 variantsMutationsViral evolutionSARS-CoV-2Viral pathogensMutation profilesVariantsImmune evasionSequenceMutation spotsPredictive language modelViral mutationsLanguage modelStrainViral infectionSemantic representationDiverse phage communities are maintained stably on a clonal bacterial host
Pyenson N, Leeks A, Nweke O, Goldford J, Schluter J, Turner P, Foster K, Sanchez A. Diverse phage communities are maintained stably on a clonal bacterial host. Science 2024, 386: 1294-1300. PMID: 39666794, PMCID: PMC7617280, DOI: 10.1126/science.adk1183.Peer-Reviewed Original ResearchConceptsPhage communitiesBacterial hostsPhage speciesEcology of bacteriophagesDiverse biological entitiesPhage diversityGrowth phenotypeCommunity ecologyEcological mechanismsPhageBacterial cellsPhenotypic heterogeneityHost populationsBacteriophageBiological entitiesDiversityHostSpeciesPhylogeneticallyNichePhenotypeStrainCellsCommunityAntibiotic resistance and draft genome profiles of 10 Streptococcus pneumoniae and 3 Streptococcus pseudopneumoniae strains isolated from the nasopharynx of people living with human immunodeficiency virus in Ghana
Ativi L, Adusei-Poku M, Boateng W, Owusu-Nyantantakyi C, Danso J, Oclu A, Bortey A, Amuasi G, Tabi B, Paintsil E, Torpey K, Dayie N, Egyir B. Antibiotic resistance and draft genome profiles of 10 Streptococcus pneumoniae and 3 Streptococcus pseudopneumoniae strains isolated from the nasopharynx of people living with human immunodeficiency virus in Ghana. Microbiology Resource Announcements 2024, 13: e00505-24. PMID: 39365088, PMCID: PMC11556032, DOI: 10.1128/mra.00505-24.Peer-Reviewed Original ResearchAntimicrobial resistanceWhole-genome profilingGenomic dataAntibiotic resistanceBacteria speciesStreptococcus pneumoniae</i>Streptococcus speciesGenomic profilingHuman immunodeficiency virusSpeciesStreptococcus pneumoniaeAntimicrobial resistance surveillance effortsImmunodeficiency virusSurveillance effortsMiddle-income countriesStrainResistanceImproved methods for genetic manipulation of the alkaliphile Halalkalibacterium halodurans
Wencker F, Lyon S, Breaker R. Improved methods for genetic manipulation of the alkaliphile Halalkalibacterium halodurans. Frontiers In Microbiology 2024, 15: 1465811. PMID: 39360312, PMCID: PMC11445130, DOI: 10.3389/fmicb.2024.1465811.Peer-Reviewed Original ResearchEnvironmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages
Shridhar S, Beghini F, Alexander M, Singh A, Juárez R, Brito I, Christakis N. Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages. Cell Reports 2024, 43: 114442. PMID: 38968070, PMCID: PMC11290354, DOI: 10.1016/j.celrep.2024.114442.Peer-Reviewed Original ResearchGut microbiomeGut microbiome speciesSpecies-level profilingSequenced microbiomesMetagenomic dataMicrobiome speciesHost phenotypeBacterial speciesHuman phenotypesMesoamerican highlandsSeveral speciesGutSpeciesMicrobiomePhenotypeAssociated with body mass indexCommunity-based cohortBody mass indexConsistent with previous findingsSocioeconomic factorsIsolated villagesHousehold wealthMass indexHostStrainAn atlas of human vector-borne microbe interactions reveals pathogenicity mechanisms
Hart T, Sonnert N, Tang X, Chaurasia R, Allen P, Hunt J, Read C, Johnson E, Arora G, Dai Y, Cui Y, Chuang Y, Yu Q, Rahman M, Mendes M, Rolandelli A, Singh P, Tripathi A, Ben Mamoun C, Caimano M, Radolf J, Lin Y, Fingerle V, Margos G, Pal U, Johnson R, Pedra J, Azad A, Salje J, Dimopoulos G, Vinetz J, Carlyon J, Palm N, Fikrig E, Ring A. An atlas of human vector-borne microbe interactions reveals pathogenicity mechanisms. Cell 2024, 187: 4113-4127.e13. PMID: 38876107, PMCID: PMC11959484, DOI: 10.1016/j.cell.2024.05.023.Peer-Reviewed Original ResearchCell invasionHost-microbe interactionsArthropod-borne pathogensHost sensingMicrobe interactionsTranscriptional regulationLyme disease spirocheteMicrobial interactionsExtracellular proteinsMicrobial pathogenesisEpidermal growth factorTissue colonizationEnvironmental cuesBacterial selectivityIntracellular pathogensPutative interactionsNext-generation therapeuticsPathogensFunctional investigationsInteractomeVector-borne diseasesImmune evasionPathogenic mechanismsStrainUnmet medical needPyrroloquinoline quinone production defines the ability of Devosia species to degrade deoxynivalenol
Guo C, Wen J, Sun Y, Liang G, Wang Z, Pan L, Huang J, Liao Y, Wang Z, Chen Q, Mu P, Deng Y. Pyrroloquinoline quinone production defines the ability of Devosia species to degrade deoxynivalenol. Food & Function 2024, 15: 6134-6146. PMID: 38767386, DOI: 10.1039/d4fo00024b.Peer-Reviewed Original ResearchPyrroloquinoline quinone productionPyrroloquinoline quinoneProduction of deoxynivalenolHEK293T cellsGenome comparisonDevosia speciesGene clusterDegradation activitySynthesis genesCompound C.Contaminates cereal cropsAnimal feed industryDON detoxificationDegrading bacteriumSynthesis abilityCell viability assayDegrading strainsDegrading bacteriaCereal cropsAnimal feedFeed industryCulture mediumGenesDeoxynivalenol degradationStrainThe recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova
Chitwood M, Colijn C, Yang C, Crudu V, Ciobanu N, Codreanu A, Kim J, Rancu I, Rhee K, Cohen T, Sobkowiak B. The recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova. Nature Communications 2024, 15: 2962. PMID: 38580642, PMCID: PMC10997638, DOI: 10.1038/s41467-024-47282-9.Peer-Reviewed Original ResearchConceptsMDR M. tuberculosisGenome sequenceResistance-conferring mutationsBeijing sublineageMDR strainsReproductive fitnessBeijing strainsCulture-positive casesLineagesMTB strainsMultidrug-resistant tuberculosisMDRMtbStrainMDR-TBMutationsResistant tuberculosisMDR-MTBSubstantial riskSublineagesTuberculosisSequenceIdentifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model
Lan Y, Crudu V, Ciobanu N, Codreanu A, Chitwood M, Sobkowiak B, Warren J, Cohen T. Identifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model. EBioMedicine 2024, 102: 105085. PMID: 38531172, PMCID: PMC10987885, DOI: 10.1016/j.ebiom.2024.105085.Peer-Reviewed Original ResearchConceptsPatterns of spatial aggregationMTB strainsMDR-TBLogistic regression modelsGenome Epidemiology StudySpecific strainsMultidrug-resistant tuberculosisTreated TB casesNational Institute of AllergyMDR phenotypeRegression modelsM. tuberculosisInstitute of AllergyMultinomial logistic regression modelUS National Institutes of HealthNational Institutes of HealthMDR diseasePublic health concernAssociated with local transmissionIncident TBInstitutes of HealthMtbResistant tuberculosisStrainDiagnosing TBComprehensive Assessment of Inactivation Methods for Madariaga Virus
Boytz R, Keita K, Pawlak J, Laurent-Rolle M. Comprehensive Assessment of Inactivation Methods for Madariaga Virus. Viruses 2024, 16: 206. PMID: 38399982, PMCID: PMC10892135, DOI: 10.3390/v16020206.Peer-Reviewed Original ResearchConceptsEastern equine encephalitis virusMadariaga virusMethod of inactivationInactivation methodSelective agentNorth American strainsEEEV strainsEquine encephalitis virusTRIzol LSAmino acid levelsAmerican strainsEncephalitis virusAcid levelsTRIzolInfected cellsVirusFormalinInactivationPathogensPublic health threatInfected supernatantStrain
2023
Sis2 regulates yeast replicative lifespan in a dose-dependent manner
Ölmez T, Moreno D, Liu P, Johnson Z, McGinnis M, Tu B, Hochstrasser M, Acar M. Sis2 regulates yeast replicative lifespan in a dose-dependent manner. Nature Communications 2023, 14: 7719. PMID: 38012152, PMCID: PMC10682402, DOI: 10.1038/s41467-023-43233-y.Peer-Reviewed Original ResearchConceptsYeast replicative lifespanReplicative lifespanRNA-seq experimentsCoenzyme A biosynthesis pathwayYeast lifespanYeast strainsStrain librariesLifespan regulationRNA-seqGene networksDose-dependent mannerLifespan extensionTranscriptional increaseYeastLifespan measurementsWild-typeGenesMachinery componentsStrainMicrofluidic platformApplications of microfluidic platformsLifespanDeletionCoenzymePathway
2022
Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs
Pennings P, Ogbunugafor C, Hershberg R. Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs. G3: Genes, Genomes, Genetics 2022, 12: jkac190. PMID: 35920784, PMCID: PMC9434179, DOI: 10.1093/g3journal/jkac190.Peer-Reviewed Original ResearchConceptsCompensatory mutationsPopulation geneticsExperimental evolutionDynamics of adaptationMutation rateWild typeEvolution of antibiotic resistanceQuality of mutationsTheoretical population geneticsDynamics of compensationEvolution of mutationsMutation supplyMicrobial evolutionNonmutant strainsProbability of reversalMutated strainsEvolutionary dynamicsFitness costsAntibiotic resistanceFitness effectsMutationsAdaptive dynamicsGeneticsStrainPotential roleAGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite
Skoufos G, Almodaresi F, Zakeri M, Paulson J, Patro R, Hatzigeorgiou A, Vlachos I. AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite. Genome Biology 2022, 23: 39. PMID: 35101114, PMCID: PMC8802518, DOI: 10.1186/s13059-022-02610-4.Peer-Reviewed Original Research
2012
A framework for human microbiome research
Methé B, Nelson K, Pop M, Creasy H, Giglio M, Huttenhower C, Gevers D, Petrosino J, Abubucker S, Badger J, Chinwalla A, Earl A, FitzGerald M, Fulton R, Hallsworth-Pepin K, Lobos E, Madupu R, Magrini V, Martin J, Mitreva M, Muzny D, Sodergren E, Versalovic J, Wollam A, Worley K, Wortman J, Young S, Zeng Q, Aagaard K, Abolude O, Allen-Vercoe E, Alm E, Alvarado L, Andersen G, Anderson S, Appelbaum E, Arachchi H, Armitage G, Arze C, Ayvaz T, Baker C, Begg L, Belachew T, Bhonagiri V, Bihan M, Blaser M, Bloom T, Bonazzi V, Brooks P, Buck G, Buhay C, Busam D, Campbell J, Canon S, Cantarel B, Chain P, Chen I, Chen L, Chhibba S, Chu K, Ciulla D, Clemente J, Clifton S, Conlan S, Crabtree J, Cutting M, Davidovics N, Davis C, DeSantis T, Deal C, Delehaunty K, Dewhirst F, Deych E, Ding Y, Dooling D, Dugan S, Dunne W, Durkin A, Edgar R, Erlich R, Farmer C, Farrell R, Faust K, Feldgarden M, Felix V, Fisher S, Fodor A, Forney L, Foster L, Di Francesco V, Friedman J, Friedrich D, Fronick C, Fulton L, Gao H, Garcia N, Giannoukos G, Giblin C, Giovanni M, Goldberg J, Goll J, Gonzalez A, Griggs A, Gujja S, Haas B, Hamilton H, Harris E, Hepburn T, Herter B, Hoffmann D, Holder M, Howarth C, Huang K, Huse S, Izard J, Jansson J, Jiang H, Jordan C, Joshi V, Katancik J, Keitel W, Kelley S, Kells C, Kinder-Haake S, King N, Knight R, Knights D, Kong H, Koren O, Koren S, Kota K, Kovar C, Kyrpides N, La Rosa P, Lee S, Lemon K, Lennon N, Lewis C, Lewis L, Ley R, Li K, Liolios K, Liu B, Liu Y, Lo C, Lozupone C, Lunsford R, Madden T, Mahurkar A, Mannon P, Mardis E, Markowitz V, Mavrommatis K, McCorrison J, McDonald D, McEwen J, McGuire A, McInnes P, Mehta T, Mihindukulasuriya K, Miller J, Minx P, Newsham I, Nusbaum C, O’Laughlin M, Orvis J, Pagani I, Palaniappan K, Patel S, Pearson M, Peterson J, Podar M, Pohl C, Pollard K, Priest M, Proctor L, Qin X, Raes J, Ravel J, Reid J, Rho M, Rhodes R, Riehle K, Rivera M, Rodriguez-Mueller B, Rogers Y, Ross M, Russ C, Sanka R, Sankar P, Sathirapongsasuti J, Schloss J, Schloss P, Schmidt T, Scholz M, Schriml L, Schubert A, Segata N, Segre J, Shannon W, Sharp R, Sharpton T, Shenoy N, Sheth N, Simone G, Singh I, Smillie C, Sobel J, Sommer D, Spicer P, Sutton G, Sykes S, Tabbaa D, Thiagarajan M, Tomlinson C, Torralba M, Treangen T, Truty R, Vishnivetskaya T, Walker J, Wang L, Wang Z, Ward D, Warren W, Watson M, Wellington C, Wetterstrand K, White J, Wilczek-Boney K, Wu Y, Wylie K, Wylie T, Yandava C, Ye L, Ye Y, Yooseph S, Youmans B, Zhang L, Zhou Y, Zhu Y, Zoloth L, Zucker J, Birren B, Gibbs R, Highlander S, Weinstock G, Wilson R, White O. A framework for human microbiome research. Nature 2012, 486: 215-221. PMID: 22699610, PMCID: PMC3377744, DOI: 10.1038/nature11209.Peer-Reviewed Original ResearchConceptsHigh-throughput metagenomic dataRibosomal RNA genesMicrobial taxonomic profilesHuman microbiome researchMetagenomic dataRNA genesTaxonomic profilesMetagenomic sequencingMetagenomics protocolHuman microbiomeMicrobiome researchMicrobial communitiesMicrobiomeGenesDistinct typesBody sitesSequenceHuman healthProject consortiumAbundanceStrain
2005
Variation in IL-1β gene expression is a major determinant of genetic differences in arthritis aggressivity in mice
Ohmura K, Johnsen A, Ortiz-Lopez A, Desany P, Roy M, Besse W, Rogus J, Bogue M, Puech A, Lathrop M, Mathis D, Benoist C. Variation in IL-1β gene expression is a major determinant of genetic differences in arthritis aggressivity in mice. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 12489-12494. PMID: 16113081, PMCID: PMC1194932, DOI: 10.1073/pnas.0504325102.Peer-Reviewed Original ResearchConceptsInbred strainsWhole-genome scanQuantitation of transcriptsInterleukin-1 gene familyConventional inbred strainsWild-derived strainsComplex genetic controlSequence haplotypesGenomic regionsGenetic lociNoncoding polymorphismsCandidate genesGenetic analysisGenetic differencesBALB/c haplotypeGenetic controlGene expressionIL-1B gene expressionBreeding strategiesBreeding schemesIL1B geneGenesSerum-transfer arthritisStrainHigh-responder BALB/c
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